I was hoping this would be fixed, as it is an issue with CS5 as well, but it has not changed in this beta.
Say I have three shape layers on the canvas.
I add each shape to its own group.
I then select all three groups and change the opacity to 50%.
The top two groups (in the layer order) will change the group opacity to 50% AND the nested shape layer to 50%, effectively making the nested shape layer 25%.
The bottom most group changes ONLY the group to 50% and not the nested shape, meaning the nested shape has an effective opacity of 50%.
It doesn't seem logical to treat identical groups in different ways so I can only assume this is a bug.
As an aside, I don't see why changing multiple group opacities needs to result in the alteration of nested items. I can't see any practical situations where this would be useful, in fact I personally find it frustrating. In the end I simply select the groups individually to change opacities, one by one, which pretty much renders the utility of simultaneously editing groups redundant... My 2 cents.
Specifically to Pierre's point, are the groups collapsed when they are selected (i.e. the child layers hidden in the collapsed group). More details (step by step) would be useful.
A screen shot of the layer selection prior and after the command or a full video of your process could be useful :
Hi, hopefully this clears it up. (might want to fullscreen for detail, of course)
This only seems to happen when selecting collapsed folders. I find it odd that it affects the bottom most folder differently.
On expanded folders selecting everything (folders plus contents) or just the contents gives the same result